For a lot of small and even medium-size C projects, one file is enough. IMHO having dozens of tiny files with only a few dozen lines each is an antipattern.
How many LOC is "medium" in your view? Most devs I work with would only put a thousand lines of code in a single file (obviously subjective, depends on density, comments etc). I'd still consider that a toy app, as opposed to my medium mark at about 100k LOC. At that stage you certainly benefit from all the tooling you seem to eschew. "Large" projects (the likes of Linux and Chromium) have so much mass they tend to have fully customized build systems.
I wrote my first Java code in Notepad and compiled it from command.com (as Windows 9x still called it). It was... fine, I guess? For the era? Not what I would want to do but far from unmanageable.
